CLAM.lite_aligner.py 文件源码

def write_parameter_log(options, args, output_dir):
    """
    Write paramter values to a log file, named by current time.
    """
    with open(output_dir+'/CLAM_Aligner.Log.'+ strftime("%Y%m%d_%H%M") + '.txt', 'w') as log:
        log.write('CLAM Re-aligner ' + __version__ + '\n')
        log.write('Args:\n' + '\n'.join(args) + '\n')
        log.write('resume: ' + str(options.resume) + '\n')
        log.write('verbose: ' + str(options.verbose) + '\n')
        log.write('output_dir: ' + str(options.output_dir) + '\n')
        log.write('tmp_dir: ' + str(options.tmp_dir) + '\n')
        log.write('window_size: ' + str(options.window_size) + '\n')
        log.write('max_multihits: ' + str(options.max_multihits) + '\n')
        log.write('is_stranded: ' + str(options.is_stranded) + '\n')
        log.write('max-gap: ' + str(options.max_gaps) + '\n')
        #log.write('gtf: ' + str(options.gtf) + '\n')
        #if len(args)>1:
        #   log.write('cov_site_min: ' + str(options.cov_site_min) + '\n')
        #   log.write('cov_gene_min: ' + str(options.cov_gene_min) + '\n')
    return